WASHINGTON — Lt. Gen. Michael T. Flynn, President-elect Donald J. Trump’s choice for national security adviser, traveled to Moscow about a year after he took charge of the Defense Intelligence Agency to cultivate what he saw as natural allies in the fight against Islamist militants: Russia’s spy agencies.

It was June 2013, a briefly optimistic moment for both the Americans and Russians, and Mr. Flynn hoped to take advantage of it. During the trip, he met with the chief of the Russian military intelligence unit known as the G.R.U. — the same agency that has since been implicated in interference in the 2016 presidential election — and held an hourlong discussion with midranking officers at its headquarters.

Relations with Moscow have soured significantly since then, yet Mr. Flynn has grown only more vehement about the need for the United States to cultivate Russia as an ally. He even returned to Moscow in 2015, a year after he was forced into retirement from the Defense Intelligence Agency, to give a paid speech for RT, the Russian English-language news organization, which American intelligence agencies have deemed a propaganda tool in the Russian election-meddling.

During that trip he also tried repeatedly to meet officers at the C.I.A’s station in Moscow — housed inside the American Embassy — to press for closer ties with Russia’s spies. But C.I.A. officers in Moscow, who have an adversarial relationship with Russia, declined to meet with him.

Now, as Mr. Flynn, 58, prepares to play a leading role in setting national security priorities in the Trump White House, his pro-Russian tilt stands in striking opposition to the judgments of the intelligence agencies he will help oversee. In an extraordinary report released last week, the agencies bluntly accused the Russian government of having worked to undermine American democracy and promote the candidacy of Mr. Trump.

The report is likely to renew questions about Mr. Flynn’s avowed eagerness to work with Russia, and his dismissal of concerns about President Vladimir V. Putin, which have at times exceeded even that of Mr. Trump himself. Neither has shown any indication of being swayed by the intelligence report on Russian meddling, and the two will within weeks be in a position to reorder American priorities in favor of closer ties with Moscow.

Any shift toward Moscow would very likely put the new administration in direct conflict with senior military commanders and intelligence officials, as well as powerful Republicans, like Senator John McCain of Arizona, the chairman of the Armed Services Committee. It may also rankle some of Mr. Trump’s own cabinet nominees — Gen. James N. Mattis, his choice for defense secretary, and Representative Mike Pompeo of Kansas, the nominee for C.I.A. director, pushed the Obama administration to take a harder line on Russia.

It appears unlikely they will get that from a Trump White House. Mr. Flynn, who is seen as particularly close to Mr. Trump and will serve as a crucial gatekeeper to the president, has said that building ties with Moscow is a strategic necessity to win what he considers a “world war” against Islamist militants.

“What we both have is a common enemy,” Mr. Flynn said in an interview in October. “The common enemy that we have is radical Islam.”

But Mr. Flynn is not always slavishly pro-Russian. He grouped Russia among the enemies of the United States in his book, “The Field of Fight,” which was published in July. In the October interview, which was conducted after American officials first accused Russia of meddling in the 2016 election, he said, “Do I want Russia to influence our election? Absolutely not.”

But Mr. Flynn, who has not responded to requests for comment since the election, then took a tack straight from Mr. Trump’s playbook: He quickly shifted to questioning the evidence of Russian meddling before dismissing it.

The real problem, he said, was that Mr. Putin respects only strength, and that the United States had behaved like a weakling under President Obama.

That would change under Mr. Trump, Mr. Flynn said. Mr. Trump understood that the danger posed by “radical Islamic terrorism” was paramount, and that Russia could help bring Iran into line and stabilize the Middle East, Mr. Flynn said.

“We can’t do what we want to do unless we work with Russia, period,” Mr. Flynn said.

A Trump administration would not be the first to try to reset relations with Russia. President George W. Bush and Mr. Obama sought to do the same early in their presidencies, though both approached the issue with more skepticism. Neither succeeded.

Russia in the meantime has grown far more aggressive. Gen. Joseph F. Dunford Jr. of the Marine Corps, the chairman of the Joint Chiefs of Staff, and Gen. Paul J. Selva of the Air Force, the vice chairman, have said that Russia potentially poses an existential threat to the United States, and that Islamist militants do not.

Nevertheless, Mr. Trump and Mr. Flynn have offered a far more positive view of working with Russia than their predecessors. As recently as this summer, Mr. Flynn spoke glowingly of his visit to the G.R.U. headquarters.

“I had a great trip. I was the first U.S. officer ever allowed inside the headquarters of the G.R.U.,” he said in an interview with The Washington Post in August.

“I was able to brief their entire staff. I gave them a leadership OPD,” he added, using a military abbreviation for a professional development class. He and the G.R.U. officers “talked a lot about the way the world’s unfolding.”

Brig. Gen. Peter Zwack, a retired Army officer who was the American military attaché in Moscow at the time of the visit, said Mr. Flynn was not blind to the pitfalls of forging closer ties to Russia. He saw areas of mutual interest, as did many others in the United States at the time, but was always firm in advancing the American position in areas where there was disagreement, General Zwack said.

“There was nothing kumbaya about these talks at all,” he said. “It was a question of finding common ground on this big, complex, fractious and increasingly dangerous planet.”

Others, though, were more skeptical of Mr. Flynn’s efforts. David Rubincam, who was the Federal Bureau of Investigation’s top agent in Moscow between 2011 and 2012, said it was clear the Russians had little interest in greater cooperation.

“The hard stuff was hard but they made the simple stuff hard. There was always a concern: Did they have a secondary agenda? We had to be cautious on sharing information.” Mr. Rubincam said. After Mr. Putin was re-elected in March 2012, “the atmosphere became increasingly toxic.”

For most American officials, any lingering hopes of closer ties were finally dashed when Russia invaded Crimea in early 2014 and the Obama administration imposed new sanctions on Moscow.

Even then, though, Mr. Flynn pushed to maintain a dialogue with Russian military intelligence. In early March 2014, when he headed the Defense Intelligence Agency and American officials were weighing sanctions, he was making plans to meet with Russian officials later that month. When his superiors found out about his plans, they ordered the meeting canceled.

The intelligence agencies’ report on Russian meddling presents an especially awkward development for Mr. Flynn by indirectly casting a harsh spotlight on his relationship with RT. It includes a lengthy and damning assessment of the network, describing it as “the Kremlin’s principal international propaganda outlet.”

Mr. Flynn has appeared repeatedly on RT, and his paid speaking engagement in December 2015 also included an invitation to the network’s lavish anniversary party. There, he was photographed sitting at the elbow of Mr. Putin.

Mr. Flynn said in October that he went to Moscow only to continue pressing for better relations.

“I basically told the audience that I thought that Russia should get Iran to back out of the proxy wars that Iran is running so we could stabilize the Middle East,” he said.

“That was my whole purpose for going,” he said. “I wasn’t there to kowtow to Putin.”

The report also said that RT is almost entirely financed by the Kremlin, which spends at least $190 million a year on RT’s broadcasting infrastructure alone. If that is accurate, Mr. Flynn’s speaking engagement could violate the emoluments clause of the Constitution, which prohibits officials from accepting anything of value from foreign governments and covers retired military officers.

Though the report was released only Friday, much of the material in it about RT comes from a report that American intelligence officials prepared in 2012, when Mr. Flynn was director of the Defense Intelligence Agency. Its view of RT as a Russian propaganda outlet has been widely shared by American officials for years.

But not Mr. Flynn, apparently. In the interview with The Post this summer, he argued that it differed little from American television news networks.

“What’s CNN? What’s MSNBC? Come on!” he said.

A version of this article appears in print on , on Page A12 of the New York edition with the headline: National Security Pick Sees Russia as Ally to Combat Islamists. Order Reprints | Today’s Paper | Subscribe